I have cca 25 databases which I need to consolidate into 1 database. First I tried to build a ssis package which would copy all data from each table into one place but then
You might run into memory issues if your Lookup transformation is set to Full cache. From what I have seen, the Merge Join performs better than Lookup transformation if the number of rows exceed 10 million.
Have a look at the following where I have explained the differences between Merge Join and Lookup transformation.
What are the differences between Merge Join and Lookup transformations in SSIS?
I found a solution and the problem was in SQL Server - it was consuming too much of memory. By default max server memory was set to 2147483647 (this is default value). Since my server has 4gb RAM, I limited this number to 1100 mb. Since then, there were no memory problems, but still, my flow tasks were very slow. The problem was in using Lookup. By default, Lookup selects everything from Lookup table - I changed this and selected only columns I need for lookup - it fastened the process several times.
Now the whole process of consolidation takes about 1:15h.